Antibodies specific to histones and to non-histone chromosomal proteins have been used to study the structure-function relation of defined proteins in chromatin and chromosomes. A sensitive and convenient enzyme linked immunoassay for analysis of these proteins has been developed. The antibody levels against chromosomal proteins in 50 patients suffering from autoimmune diseases has been determined. Antibodies to the globular region of histone H5 have been elicited. Microinjection of antibodies to histone H2B and non-histone HMG-1 into the nuclei of oocytes of Pleurodeles waltlii bring about a specific retraction of the transcriptional loops in the lampbrush chromosomes present in these oocytes. Microinjection of antibody fragments into the nucleus and cytoplasm of somatic cells indicate that F(ab)2 does, but IgG does not, transverse the nuclear membrane. Histone antigenic determinants are masked in the transcriptionally active regions of polytene chromosomes.